This is an analysis of differential expression at the transcript level between treatment groups for control and infected blue-winged teal ileum samples.
## Load packages and data
library(limma)
library(edgeR)
library(Glimma)
library(gplots)
library(ggrepel)
library(RColorBrewer)
library(gridExtra)
library(kableExtra)
library(topGO)
library(clusterProfiler)
library(tidyverse)
## Load data
annot <- read.delim("G:/Shared drives/RNA Seq Supershedder Project/BWTE DE manuscript/extData/Trinotate.csv", header = TRUE, sep = "\t")
cnt <- read.table("G:/Shared drives/RNA Seq Supershedder Project/BWTE DE manuscript/extData/rsem.isoform.counts.matrix", header = TRUE)
covars <- read.csv("G:/Shared drives/RNA Seq Supershedder Project/BWTE DE manuscript/extData/BWTE54_SSgroup_Raw_Pool.csv", header = TRUE)
Bird 36 is missing a measurement for the weight covariate and bird 19 had improper tissue-based grouping, suggesting a potential sample mix up. They are both removed from the analysis. We also rename the transcripts, dropping the “Trinity_” prefix.
cnt <- cnt %>%
select(
-alignEstimateAbundance_BWTE_Ileum_36_S50,
-alignEstimateAbundance_BWTE_Bursa_36_S31,-alignEstimateAbundance_BWTE_Ileum_19_S35,
-alignEstimateAbundance_BWTE_Bursa_19_S14) %>%
rownames_to_column("transcript") %>%
separate(transcript, into = c(NA, "pt1", "pt2", "gene", "isoform")) %>%
unite(transcript, pt1, pt2, gene, isoform) %>%
column_to_rownames("transcript") %>%
select(contains("Ileum"))
covars <- covars %>%
filter(!bird %in% c("36", "19")) %>%
arrange(bird) %>%
mutate(group = str_remove(group, "-"))
annot <- annot %>%
separate(transcript_id, into = c(NA, "pt1", "pt2", "gene", "isoform")) %>%
unite(transcript_id, pt1, pt2, gene, isoform)
bird <- as.factor(covars$bird)
sex <- as.factor(covars$sex)
age <- as.numeric(covars$age)
weight <- covars$wt_55
group <- recode(covars$group, C1 = "Ctl", C14 = "Ctl") %>%
as.factor()
pool <- as.factor(covars$Pool.Ileum)
Here we standardize expression levels across samples of varying depth by using the counts per million (CPM) and trimmed mean of M-values (TMM) methods. We also remove any transcripts that are expressed at few than 0.5 CPM in at least 25% of individuals.
#Convert to DGEList object
dge <- DGEList(counts=cnt)
dge$genes <- annot[match(rownames(dge$counts), annot$transcript_id),]
#CPM and log-CPM
cpm <- cpm(dge)
lcpm <- cpm(dge, log = TRUE)
#### Retain only transcripts expressed at >0.5 CPM in at least 25% of individuals
table(rowSums(dge$counts==0) == length(cnt[1,]))
##
## FALSE TRUE
## 484888 86217
keep.exprs <- rowSums(cpm>0.5) >= length(cnt[1,])/4
sum(keep.exprs)
## [1] 66980
dge <- dge[keep.exprs,, keep.lib.sizes=FALSE]
table(rowSums(dge$counts==0) == length(cnt[1,]))
##
## FALSE
## 66980
dim(dge)
## [1] 66980 52
#TMM normalization
dge <- calcNormFactors(dge, method = "TMM")
Multidimensional scaling (MDS) plots are an ordination technique that lets us examine sample clustering based on overall gene expression levels.
col.group = as.numeric(as.factor(paste0(group)))
plotMDS(lcpm, labels = paste0(bird, "_", group), col = col.group, cex = 0.75)
title(main="Treatment group")
## Establish design matrix
design = model.matrix(~ 0 +
group +
age +
sex +
weight +
pool)
colnames(design) <- gsub("group", "", colnames(design))
contr.matrix = makeContrasts(
CtlvI1 = Ctl - I1,
CtlvI3 = Ctl - I3,
CtlvI5 = Ctl - I5,
CtlvI14 = Ctl - I14,
I1vI3 = I1 - I3,
I3vI5 = I3 - I5,
I5vI14 = I5 - I14,
levels = colnames(design))
v <- voomWithQualityWeights(dge, design, plot = TRUE)
vfit <- lmFit(v, design)
vfit <- contrasts.fit(vfit, contrasts = contr.matrix)
tfit <- treat(vfit, lfc = 1.0)
plotSA(tfit)
For a transcript to be considered differentially expressed, we require a p-value of 0.1 with a false discovery rate correction and a log fold count difference of 1.
dt <- decideTests(tfit, p.value = 0.1, adjust.method = "fdr")
summary(dt) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = F)
| CtlvI1 | CtlvI3 | CtlvI5 | CtlvI14 | I1vI3 | I3vI5 | I5vI14 | |
|---|---|---|---|---|---|---|---|
| Down | 58 | 27 | 0 | 0 | 0 | 1 | 0 |
| NotSig | 66915 | 66947 | 66980 | 66979 | 66979 | 66979 | 66979 |
| Up | 7 | 6 | 0 | 1 | 1 | 0 | 1 |
dt.tib <- as_tibble(dt, rownames = NA) %>%
rownames_to_column("transcript") %>%
mutate_at(vars(starts_with("C")), as.numeric) %>%
mutate_at(vars(starts_with("I")), as.numeric) %>%
filter_at(vars(CtlvI1:I5vI14), any_vars(. != 0))
hist(tfit$p.value, main = "P-values comparing groups (eBayes)")
tmp1 <- topTreat(tfit, coef = 1, n = Inf)
results1 <- mutate(tmp1, sig=ifelse(tmp1$adj.P.Val<0.1, "Sig", "Not Sig"))
p1 <- ggplot(results1, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Control vs. Infected, Day 1") +
ylab("-Log10(Adjusted p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
tmp2 <- topTreat(tfit, coef = 2, n = Inf)
results2 <- mutate(tmp2, sig=ifelse(tmp2$adj.P.Val<0.1, "Sig", "Not Sig"))
p2 <- ggplot(results2, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Control vs. Infected, Day 3") +
ylab("-Log10(Adjusted p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
tmp3 <- topTreat(tfit, coef = 3, n = Inf)
results3 <- mutate(tmp3, sig=ifelse(tmp3$adj.P.Val<0.1, "Sig", "Not Sig"))
p3 <- ggplot(results3, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Control vs. Infected, Day 5") +
ylab("-Log10(Adjusted p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
tmp4 <- topTreat(tfit, coef = 4, n = Inf)
results4 <- mutate(tmp4, sig=ifelse(tmp4$adj.P.Val<0.1, "Sig", "Not Sig"))
p4 <- ggplot(results4, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Control vs. Infected, Day 14") +
ylab("-Log10(Adjusted p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
tmp5 <- topTreat(tfit, coef = 5, n = Inf)
results5 <- mutate(tmp5, sig=ifelse(tmp5$adj.P.Val<0.1, "Sig", "Not Sig"))
p5 <- ggplot(results5, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Infected, Day 1 vs. Infected, Day 3") +
ylab("-Log10(Adjusted p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
tmp6 <- topTreat(tfit, coef = 6, n = Inf)
results6 <- mutate(tmp6, sig=ifelse(tmp6$adj.P.Val<0.1, "Sig", "Not Sig"))
p6 <- ggplot(results6, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Infected, Day 3 vs. Infected, Day 5") +
ylab("-Log10(Adjusted p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
tmp7 <- topTreat(tfit, coef = 7, n = Inf)
results7 <- mutate(tmp7, sig=ifelse(tmp7$adj.P.Val<0.1, "Sig", "Not Sig"))
p7 <- ggplot(results7, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Infected, Day 5 vs. Infected, Day 14") +
ylab("-Log10(Adjusted p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
grid.arrange(p1, p2, p3, p4, p5, p6, p7, nrow = 4)
# Get the gene names for DE genes
deGeneCounts <- lcpm %>%
as_tibble(rownames = NA) %>%
rownames_to_column("transcript") %>%
filter(transcript %in% dt.tib$transcript) %>%
column_to_rownames("transcript")
group2 <- group %>%
as_tibble() %>%
mutate(group = sub("I3", "I03", value)) %>%
mutate(group = sub("I1", "I01", group)) %>%
mutate(group = sub("I5", "I05", group)) %>%
mutate(group = sub("I014", "I14", group))
newNames1 <- colnames(deGeneCounts) %>%
as_tibble() %>%
separate(value, into = c(NA, NA, NA, "sample", NA)) %>%
mutate(group = group2$group) %>%
unite("sample", 2:1, sep = "_")
colnames(deGeneCounts) <- newNames1$sample
deGeneCounts <- deGeneCounts %>% dplyr::select(order(colnames(.))) %>%
as.matrix()
heatmap.annot <- annot %>%
select(
transcript_id,
sprot_Top_BLASTX_hit) %>%
filter(transcript_id %in% dt.tib$transcript) %>%
separate(sprot_Top_BLASTX_hit, into = c("SwissProt_GeneName", NA, NA, NA, NA, "sprot2", NA), "\\^") %>%
separate(sprot2, sep = "=", into = c(NA, "SwissProt_GeneFunction")) %>%
distinct(transcript_id, SwissProt_GeneName) %>%
filter(SwissProt_GeneName != ".")
deGeneCounts <- deGeneCounts %>%
as_tibble(rownames = NA) %>%
mutate(transcript = rownames(.)) %>%
rename(transcript_id = transcript) %>%
left_join(heatmap.annot) %>%
mutate(SwissProt_GeneName = replace_na(SwissProt_GeneName, ".")) %>%
unite(transcript, transcript_id:SwissProt_GeneName, sep = " - ") %>%
column_to_rownames("transcript") %>%
as.matrix()
## Set up palette
mypalette <- brewer.pal(11,"RdYlBu")
morecols <- colorRampPalette(mypalette)
hc <- hclust(as.dist(1-cor(t(deGeneCounts))))
# Plot the heatmap
heatmap.2(deGeneCounts,
Colv = FALSE,
Rowv = as.dendrogram(hc),
col = rev(morecols(50)),
trace = "none",
colsep = c(9, 21, 33, 45),
dendrogram = "row",
density.info = "none",
key = TRUE,
#main = "Ileum - Gene level",
margins = c(10, 15),
scale ="row")
lcpm.DE <- lcpm %>%
as_tibble(rownames = NA) %>%
rownames_to_column("identifier") %>%
filter(identifier %in% dt.tib$transcript) %>%
pivot_longer(cols = contains("_"),
names_to = "sample",
values_to = "lcpm") %>%
separate(sample, into = c(NA, NA, "tissue", "bird", NA)) %>%
mutate(bird = as.integer(bird)) %>%
left_join(covars, by = "bird") %>%
select(identifier, bird, lcpm, group) %>%
mutate(group = recode(group, C14 = "Control"),
group = recode(group, C1 = "Control"),
tmpID = ifelse(group == "Control", 'Control', 'Infected'))
aprioriPlotting <- function(target, ...) {
annot.target <- annot %>%
select(
transcript_id,
sprot_Top_BLASTX_hit) %>%
filter(transcript_id == target) %>%
separate(sprot_Top_BLASTX_hit, into = c("SwissProt_GeneName", NA, NA, NA, NA, NA, NA), "\\^")
plot <- lcpm.DE %>%
filter(identifier == target) %>%
mutate(group = fct_relevel(group, "Control", "I1", "I3", "I5", "I14")) %>%
ggplot(aes(x = group, y = lcpm)) +
facet_grid(. ~ tmpID, scales = "free", space = "free") +
ylab("Log2(Counts per million)") +
xlab("Group") +
geom_point(position = position_dodge(width=0.75), show.legend = FALSE) +
geom_boxplot(alpha = 0.5) +
geom_label_repel(aes(label = bird, fill = NULL), show.legend=FALSE) +
theme_classic() +
labs(title= paste0(target, " - ", annot.target[1,2])) +
theme(legend.title = element_blank())
print(plot)
}
for(trans in sort(unique(lcpm.DE$identifier))) {
aprioriPlotting(trans)
}
ns denotes non-significant transcripts for each comparison and numerical values are the log(fold count) difference
tmp1a <- tmp1 %>% select(transcript_id, adj.P.Val, logFC, sprot_Top_BLASTX_hit, Kegg) %>% separate(sprot_Top_BLASTX_hit, into = c("SwissProt_GeneName", NA, NA, NA, NA, "sprot2", NA), "\\^") %>% separate(sprot2, sep = "=", into = c(NA, "SwissProt_GeneFunction")) %>% separate(Kegg, into = c("KEGG_ID", "KO_ID"), sep = "\\`") %>% mutate(comp = "CtlvI1")
tmp2a <- tmp2 %>% select(transcript_id, adj.P.Val, logFC, sprot_Top_BLASTX_hit, Kegg) %>% separate(sprot_Top_BLASTX_hit, into = c("SwissProt_GeneName", NA, NA, NA, NA, "sprot2", NA), "\\^") %>% separate(sprot2, sep = "=", into = c(NA, "SwissProt_GeneFunction")) %>% separate(Kegg, into = c("KEGG_ID", "KO_ID"), sep = "\\`") %>% mutate(comp = "CtlvI3")
tmp3a <- tmp3 %>% select(transcript_id, adj.P.Val, logFC, sprot_Top_BLASTX_hit, Kegg) %>% separate(sprot_Top_BLASTX_hit, into = c("SwissProt_GeneName", NA, NA, NA, NA, "sprot2", NA), "\\^") %>% separate(sprot2, sep = "=", into = c(NA, "SwissProt_GeneFunction")) %>% separate(Kegg, into = c("KEGG_ID", "KO_ID"), sep = "\\`") %>% mutate(comp = "CtlvI5")
tmp4a <- tmp4 %>% select(transcript_id, adj.P.Val, logFC, sprot_Top_BLASTX_hit, Kegg) %>% separate(sprot_Top_BLASTX_hit, into = c("SwissProt_GeneName", NA, NA, NA, NA, "sprot2", NA), "\\^") %>% separate(sprot2, sep = "=", into = c(NA, "SwissProt_GeneFunction")) %>% separate(Kegg, into = c("KEGG_ID", "KO_ID"), sep = "\\`") %>% mutate(comp = "CtlvI14")
tmp5a <- tmp5 %>% select(transcript_id, adj.P.Val, logFC, sprot_Top_BLASTX_hit, Kegg) %>% separate(sprot_Top_BLASTX_hit, into = c("SwissProt_GeneName", NA, NA, NA, NA, "sprot2", NA), "\\^") %>% separate(sprot2, sep = "=", into = c(NA, "SwissProt_GeneFunction")) %>% separate(Kegg, into = c("KEGG_ID", "KO_ID"), sep = "\\`") %>% mutate(comp = "I1vI3")
tmp6a <- tmp6 %>% select(transcript_id, adj.P.Val, logFC, sprot_Top_BLASTX_hit, Kegg) %>% separate(sprot_Top_BLASTX_hit, into = c("SwissProt_GeneName", NA, NA, NA, NA, "sprot2", NA), "\\^") %>% separate(sprot2, sep = "=", into = c(NA, "SwissProt_GeneFunction")) %>% separate(Kegg, into = c("KEGG_ID", "KO_ID"), sep = "\\`") %>% mutate(comp = "I3vI5")
tmp7a <- tmp7 %>% select(transcript_id, adj.P.Val, logFC, sprot_Top_BLASTX_hit, Kegg) %>% separate(sprot_Top_BLASTX_hit, into = c("SwissProt_GeneName", NA, NA, NA, NA, "sprot2", NA), "\\^") %>% separate(sprot2, sep = "=", into = c(NA, "SwissProt_GeneFunction")) %>% separate(Kegg, into = c("KEGG_ID", "KO_ID"), sep = "\\`") %>% mutate(comp = "I5vI14")
bind_rows(tmp1a, tmp2a, tmp3a, tmp4a, tmp5a, tmp6a, tmp7a) %>%
select(-SwissProt_GeneFunction, -KEGG_ID, -KO_ID) %>%
filter(transcript_id %in% dt.tib$transcript) %>%
mutate(logFoldCount = ifelse(adj.P.Val < 0.10, round(logFC, 2), "ns")) %>%
select(-adj.P.Val, -logFC) %>%
pivot_wider(names_from = comp, values_from = logFoldCount) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
| transcript_id | SwissProt_GeneName | CtlvI1 | CtlvI3 | CtlvI5 | CtlvI14 | I1vI3 | I3vI5 | I5vI14 |
|---|---|---|---|---|---|---|---|---|
| DN2085_c0_g2_i5 | MX_ANAPL | -5.94 | -4.77 | ns | ns | ns | ns | ns |
| DN2085_c0_g2_i14 | MX_ANAPL | -7.23 | -5.74 | ns | ns | ns | ns | ns |
| DN2085_c0_g2_i11 | MX_ANAPL | -5.5 | -4.05 | ns | ns | ns | ns | ns |
| DN17179_c0_g1_i5 | ESIP1_HUMAN | -6.53 | -5.37 | ns | ns | ns | ns | ns |
| DN2085_c0_g2_i16 | MX_ANAPL | -5.24 | -4.35 | ns | ns | ns | ns | ns |
| DN614_c0_g2_i4 | CMPK2_HUMAN | -5.85 | -4.19 | ns | ns | ns | ns | ns |
| DN6590_c0_g1_i1 | TMPS2_HUMAN | -5.44 | -4.07 | ns | ns | ns | ns | ns |
| DN17179_c0_g1_i4 | ESIP1_HUMAN | -6.22 | -5.84 | ns | ns | ns | ns | ns |
| DN2085_c0_g2_i15 | MX_ANAPL | -7.03 | -5.71 | ns | ns | ns | ns | ns |
| DN428854_c0_g1_i1 | . | -4.93 | ns | ns | ns | ns | ns | ns |
| DN15897_c0_g1_i1 | NCAP_I53A0 | -11.68 | -9.93 | ns | ns | ns | ns | ns |
| DN8513_c3_g1_i1 | M1_I80AD | -10.91 | -8.96 | ns | ns | ns | ns | ns |
| DN2085_c0_g2_i10 | MX_ANAPL | -5.34 | -4.19 | ns | ns | ns | ns | ns |
| DN614_c0_g2_i1 | CMPK2_HUMAN | -5.77 | ns | ns | ns | ns | ns | ns |
| DN7314_c1_g2_i2 | HEMA_I87A1 | -10.57 | -8.37 | ns | ns | ns | ns | ns |
| DN7314_c1_g1_i2 | HEMA_I87A1 | -9.75 | -7.65 | ns | ns | ns | ns | ns |
| DN1765_c0_g1_i1 | . | -5.81 | ns | ns | ns | ns | ns | ns |
| DN43220_c0_g1_i9 | UBP18_HUMAN | -4.22 | -3.58 | ns | ns | ns | ns | ns |
| DN11336_c0_g1_i2 | NS1_I78A1 | -9.87 | -8.37 | ns | ns | ns | ns | ns |
| DN17179_c0_g1_i2 | ESIP1_HUMAN | -6.06 | -4.92 | ns | ns | ns | ns | ns |
| DN95654_c0_g1_i1 | DSG1_PIG | 4.47 | ns | ns | ns | ns | ns | ns |
| DN12097_c0_g2_i4 | NRAM_I85A8 | -9.24 | -7.44 | ns | ns | ns | ns | ns |
| DN8513_c3_g2_i1 | M2_I66A0 | -9.53 | -7.71 | ns | ns | ns | ns | ns |
| DN17249_c1_g1_i1 | TMPS2_HUMAN | -5.14 | ns | ns | ns | ns | ns | ns |
| DN3062_c0_g1_i18 | RN213_HUMAN | -4.59 | ns | ns | ns | ns | ns | ns |
| DN2198_c0_g1_i1 | DDX60_HUMAN | -5.73 | -4.75 | ns | ns | ns | ns | ns |
| DN2085_c0_g2_i13 | MX_ANAPL | -5.11 | ns | ns | ns | ns | ns | ns |
| DN591_c9_g2_i1 | . | -5.12 | ns | ns | ns | ns | ns | ns |
| DN14251_c0_g1_i13 | . | -5.83 | ns | ns | ns | ns | ns | ns |
| DN2198_c0_g1_i6 | DDX60_HUMAN | -4.54 | -3.98 | ns | ns | ns | ns | ns |
| DN6178_c0_g1_i1 | IFIT5_HUMAN | -5.06 | ns | ns | ns | ns | ns | ns |
| DN2932_c0_g1_i6 | IFI6_BOVIN | -4.77 | -5.45 | ns | ns | ns | ns | ns |
| DN1920_c0_g1_i9 | RSAD2_BOVIN | -4.72 | ns | ns | ns | ns | ns | ns |
| DN2085_c0_g2_i12 | MX_ANAPL | -5.43 | ns | ns | ns | ns | ns | ns |
| DN10817_c0_g1_i1 | RDRP_I78AC | -8.07 | ns | ns | ns | ns | ns | ns |
| DN2198_c0_g1_i10 | DDX60_HUMAN | -3.97 | -3.61 | ns | ns | ns | ns | ns |
| DN3062_c0_g1_i12 | RN213_HUMAN | -3.17 | ns | ns | ns | ns | ns | ns |
| DN2559_c0_g1_i7 | MOV10_CHICK | -5.23 | ns | ns | ns | ns | ns | ns |
| DN7633_c1_g1_i16 | BIRC6_HUMAN | 7.74 | ns | ns | ns | ns | ns | ns |
| DN1920_c0_g1_i11 | RSAD2_PIG | -4.74 | ns | ns | ns | ns | ns | ns |
| DN17714_c0_g1_i3 | PA_I78AC | -7.4 | ns | ns | ns | ns | ns | ns |
| DN4591_c0_g1_i4 | SAM9L_HUMAN | -3.16 | ns | ns | ns | ns | ns | ns |
| DN614_c0_g2_i8 | CMPK2_HUMAN | -4.6 | ns | ns | ns | ns | ns | ns |
| DN2145_c1_g1_i1 | . | -5.59 | ns | ns | ns | ns | ns | ns |
| DN9487_c0_g1_i2 | . | -4.44 | ns | ns | ns | ns | ns | ns |
| DN427_c0_g2_i4 | NOX4_PONAB | 2.88 | ns | ns | ns | ns | ns | ns |
| DN135990_c0_g1_i1 | PB2_I80A6 | -7.21 | ns | ns | ns | ns | ns | ns |
| DN2085_c0_g2_i6 | MX_ANAPL | -5.3 | ns | ns | ns | ns | ns | ns |
| DN9051_c0_g1_i3 | GA2L1_MOUSE | -5.92 | ns | ns | ns | ns | ns | ns |
| DN20874_c0_g1_i11 | PAR12_HUMAN | -2.44 | ns | ns | ns | ns | ns | ns |
| DN22_c0_g1_i2 | MIRO1_CHICK | -5.16 | ns | ns | ns | ns | ns | ns |
| DN1920_c0_g1_i1 | RSAD2_BOVIN | -6.25 | ns | ns | ns | ns | ns | ns |
| DN6190_c0_g1_i4 | OASL2_MOUSE | -5.23 | ns | ns | ns | ns | ns | ns |
| DN2767_c0_g1_i1 | ISLR_HUMAN | -5.75 | ns | ns | ns | ns | ns | ns |
| DN3062_c0_g1_i10 | RN213_HUMAN | -5.96 | ns | ns | ns | ns | ns | ns |
| DN24620_c0_g1_i11 | . | 3.66 | ns | ns | ns | ns | ns | ns |
| DN6309_c0_g1_i12 | . | -3.66 | ns | ns | ns | ns | ns | ns |
| DN166_c0_g1_i5 | RN141_CHICK | 7.59 | ns | ns | ns | ns | ns | ns |
| DN43220_c0_g1_i4 | UBP18_HUMAN | -5.61 | ns | ns | ns | ns | ns | ns |
| DN34132_c0_g1_i4 | K2C74_MOUSE | 3.55 | ns | ns | ns | ns | ns | ns |
| DN1934_c0_g1_i11 | IRF3_CHICK | -2.69 | ns | ns | ns | ns | ns | ns |
| DN17171_c0_g1_i3 | MTAP2_RAT | 4.29 | ns | ns | ns | ns | ns | ns |
| DN2293_c0_g1_i3 | PIGY_HUMAN | -5.69 | ns | ns | ns | ns | ns | ns |
| DN6190_c0_g1_i2 | OASL1_RAT | -3.73 | ns | ns | ns | ns | ns | ns |
| DN1934_c0_g1_i16 | IRF3_CHICK | -4.55 | ns | ns | ns | ns | ns | ns |
| DN5214_c0_g1_i6 | CF062_MOUSE | ns | -4.76 | ns | ns | ns | ns | ns |
| DN9772_c0_g1_i10 | UQCC2_DANRE | ns | -4.15 | ns | ns | ns | ns | ns |
| DN2228_c2_g1_i8 | BMPR2_MOUSE | ns | 5.66 | ns | ns | ns | ns | ns |
| DN4998_c0_g1_i2 | CNPY3_BOVIN | ns | -3.85 | ns | ns | ns | ns | ns |
| DN14729_c0_g1_i4 | FREM1_HUMAN | ns | 4.62 | ns | ns | ns | ns | ns |
| DN4239_c0_g1_i17 | MYCB2_MOUSE | ns | 5.72 | ns | ns | ns | ns | ns |
| DN220085_c0_g1_i2 | LAG3_MOUSE | ns | -3.47 | ns | ns | ns | ns | ns |
| DN12331_c1_g1_i3 | LRIG3_HUMAN | ns | 4.28 | ns | ns | ns | ns | ns |
| DN611_c1_g1_i6 | LRRK2_HUMAN | ns | 4.31 | ns | ns | ns | ns | ns |
| DN2458_c0_g1_i1 | DDX17_MOUSE | ns | 4.36 | ns | ns | 4.87 | ns | ns |
| DN1712_c0_g2_i10 | DCAF4_HUMAN | ns | ns | ns | 4.94 | ns | ns | 4.84 |
| DN3176_c0_g1_i11 | . | ns | ns | ns | ns | ns | -3.59 | ns |
bind_rows(tmp1a, tmp2a, tmp3a, tmp4a, tmp5a, tmp6a, tmp7a) %>%
select(-comp, -adj.P.Val, -logFC) %>%
filter(transcript_id %in% dt.tib$transcript) %>%
distinct(.) %>% filter(SwissProt_GeneName != ".") %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
| transcript_id | SwissProt_GeneName | SwissProt_GeneFunction | KEGG_ID | KO_ID |
|---|---|---|---|---|
| DN2085_c0_g2_i5 | MX_ANAPL | Interferon-induced GTP-binding protein Mx; | KEGG:apla:101793492 | KO:K14754 |
| DN2085_c0_g2_i14 | MX_ANAPL | Interferon-induced GTP-binding protein Mx; | KEGG:apla:101793492 | KO:K14754 |
| DN2085_c0_g2_i11 | MX_ANAPL | Interferon-induced GTP-binding protein Mx; | KEGG:apla:101793492 | KO:K14754 |
| DN17179_c0_g1_i5 | ESIP1_HUMAN | Epithelial-stromal interaction protein 1; | KEGG:hsa:94240 | NA |
| DN2085_c0_g2_i16 | MX_ANAPL | Interferon-induced GTP-binding protein Mx; | KEGG:apla:101793492 | KO:K14754 |
| DN614_c0_g2_i4 | CMPK2_HUMAN | UMP-CMP kinase 2, mitochondrial; | KEGG:hsa:129607 | KO:K13809 |
| DN6590_c0_g1_i1 | TMPS2_HUMAN | Transmembrane protease serine 2; | KEGG:hsa:7113 | KO:K09633 |
| DN17179_c0_g1_i4 | ESIP1_HUMAN | Epithelial-stromal interaction protein 1; | KEGG:hsa:94240 | NA |
| DN2085_c0_g2_i15 | MX_ANAPL | Interferon-induced GTP-binding protein Mx; | KEGG:apla:101793492 | KO:K14754 |
| DN15897_c0_g1_i1 | NCAP_I53A0 | Nucleoprotein {ECO:0000255|HAMAP-Rule:MF_04070}; | . | NA |
| DN8513_c3_g1_i1 | M1_I80AD | Matrix protein 1 {ECO:0000255|HAMAP-Rule:MF_04068}; | . | NA |
| DN2085_c0_g2_i10 | MX_ANAPL | Interferon-induced GTP-binding protein Mx; | KEGG:apla:101793492 | KO:K14754 |
| DN614_c0_g2_i1 | CMPK2_HUMAN | UMP-CMP kinase 2, mitochondrial; | KEGG:hsa:129607 | KO:K13809 |
| DN7314_c1_g2_i2 | HEMA_I87A1 | Hemagglutinin {ECO:0000255|HAMAP-Rule:MF_04072}; | . | NA |
| DN7314_c1_g1_i2 | HEMA_I87A1 | Hemagglutinin {ECO:0000255|HAMAP-Rule:MF_04072}; | . | NA |
| DN43220_c0_g1_i9 | UBP18_HUMAN | Ubl carboxyl-terminal hydrolase 18; | KEGG:hsa:11274 | KO:K11846 |
| DN11336_c0_g1_i2 | NS1_I78A1 | Non-structural protein 1 {ECO:0000255|HAMAP-Rule:MF_04066}; | . | NA |
| DN17179_c0_g1_i2 | ESIP1_HUMAN | Epithelial-stromal interaction protein 1; | KEGG:hsa:94240 | NA |
| DN95654_c0_g1_i1 | DSG1_PIG | Desmoglein-1; | KEGG:ssc:641355 | KO:K07596 |
| DN12097_c0_g2_i4 | NRAM_I85A8 | Neuraminidase {ECO:0000255|HAMAP-Rule:MF_04071}; | . | NA |
| DN8513_c3_g2_i1 | M2_I66A0 | Matrix protein 2 {ECO:0000255|HAMAP-Rule:MF_04069}; | . | NA |
| DN17249_c1_g1_i1 | TMPS2_HUMAN | Transmembrane protease serine 2; | KEGG:hsa:7113 | KO:K09633 |
| DN3062_c0_g1_i18 | RN213_HUMAN | E3 ubiquitin-protein ligase RNF213 {ECO:0000305}; | KEGG:hsa:57674 | KO:K22754 |
| DN2198_c0_g1_i1 | DDX60_HUMAN | Probable ATP-dependent RNA helicase DDX60; | KEGG:hsa:55601 | KO:K20103 |
| DN2085_c0_g2_i13 | MX_ANAPL | Interferon-induced GTP-binding protein Mx; | KEGG:apla:101793492 | KO:K14754 |
| DN2198_c0_g1_i6 | DDX60_HUMAN | Probable ATP-dependent RNA helicase DDX60; | KEGG:hsa:55601 | KO:K20103 |
| DN6178_c0_g1_i1 | IFIT5_HUMAN | Interferon-induced protein with tetratricopeptide repeats 5; | KEGG:hsa:24138 | NA |
| DN2932_c0_g1_i6 | IFI6_BOVIN | Interferon alpha-inducible protein 6 {ECO:0000305}; | KEGG:bta:512913 | NA |
| DN1920_c0_g1_i9 | RSAD2_BOVIN | Radical S-adenosyl methionine domain-containing protein 2; | KEGG:bta:506415 | KO:K15045 |
| DN2085_c0_g2_i12 | MX_ANAPL | Interferon-induced GTP-binding protein Mx; | KEGG:apla:101793492 | KO:K14754 |
| DN10817_c0_g1_i1 | RDRP_I78AC | RNA-directed RNA polymerase catalytic subunit {ECO:0000255|HAMAP-Rule:MF_04065}; | . | NA |
| DN2198_c0_g1_i10 | DDX60_HUMAN | Probable ATP-dependent RNA helicase DDX60; | KEGG:hsa:55601 | KO:K20103 |
| DN3062_c0_g1_i12 | RN213_HUMAN | E3 ubiquitin-protein ligase RNF213 {ECO:0000305}; | KEGG:hsa:57674 | KO:K22754 |
| DN2559_c0_g1_i7 | MOV10_CHICK | Putative helicase MOV-10; | KEGG:gga:419872 | KO:K18422 |
| DN7633_c1_g1_i16 | BIRC6_HUMAN | Baculoviral IAP repeat-containing protein 6; | KEGG:hsa:57448 | KO:K10586 |
| DN1920_c0_g1_i11 | RSAD2_PIG | Radical S-adenosyl methionine domain-containing protein 2; | KEGG:ssc:396752 | KO:K15045 |
| DN17714_c0_g1_i3 | PA_I78AC | Polymerase acidic protein {ECO:0000255|HAMAP-Rule:MF_04063}; | . | NA |
| DN4591_c0_g1_i4 | SAM9L_HUMAN | Sterile alpha motif domain-containing protein 9-like; | KEGG:hsa:219285 | NA |
| DN614_c0_g2_i8 | CMPK2_HUMAN | UMP-CMP kinase 2, mitochondrial; | KEGG:hsa:129607 | KO:K13809 |
| DN427_c0_g2_i4 | NOX4_PONAB | NADPH oxidase 4; | KEGG:pon:100171782 | KO:K21423 |
| DN135990_c0_g1_i1 | PB2_I80A6 | Polymerase basic protein 2 {ECO:0000255|HAMAP-Rule:MF_04062}; | . | NA |
| DN2085_c0_g2_i6 | MX_ANAPL | Interferon-induced GTP-binding protein Mx; | KEGG:apla:101793492 | KO:K14754 |
| DN9051_c0_g1_i3 | GA2L1_MOUSE | GAS2-like protein 1; | KEGG:mmu:78926 | NA |
| DN20874_c0_g1_i11 | PAR12_HUMAN | Protein mono-ADP-ribosyltransferase PARP12 {ECO:0000305}; | KEGG:hsa:64761 | KO:K15259 |
| DN22_c0_g1_i2 | MIRO1_CHICK | Mitochondrial Rho GTPase 1; | KEGG:gga:417410 | KO:K07870 |
| DN1920_c0_g1_i1 | RSAD2_BOVIN | Radical S-adenosyl methionine domain-containing protein 2; | KEGG:bta:506415 | KO:K15045 |
| DN6190_c0_g1_i4 | OASL2_MOUSE | 2’-5’-oligoadenylate synthase-like protein 2; | KEGG:rno:304545 | KO:K14608 |
| DN2767_c0_g1_i1 | ISLR_HUMAN | Immunoglobulin superfamily containing leucine-rich repeat protein; | KEGG:hsa:3671 | NA |
| DN3062_c0_g1_i10 | RN213_HUMAN | E3 ubiquitin-protein ligase RNF213 {ECO:0000305}; | KEGG:hsa:57674 | KO:K22754 |
| DN166_c0_g1_i5 | RN141_CHICK | RING finger protein 141; | KEGG:gga:423039 | NA |
| DN43220_c0_g1_i4 | UBP18_HUMAN | Ubl carboxyl-terminal hydrolase 18; | KEGG:hsa:11274 | KO:K11846 |
| DN34132_c0_g1_i4 | K2C74_MOUSE | Keratin, type II cytoskeletal 74 {ECO:0000250|UniProtKB:Q7RT57}; | KEGG:mmu:223917 | KO:K07605 |
| DN1934_c0_g1_i11 | IRF3_CHICK | Interferon regulatory factor 3; | KEGG:gga:396330 | KO:K09447 |
| DN17171_c0_g1_i3 | MTAP2_RAT | Microtubule-associated protein 2; | . | NA |
| DN2293_c0_g1_i3 | PIGY_HUMAN | Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y; | KEGG:hsa:84992 | KO:K11001 |
| DN6190_c0_g1_i2 | OASL1_RAT | 2’-5’-oligoadenylate synthase-like protein 1; | KEGG:rno:304545 | KO:K14608 |
| DN1934_c0_g1_i16 | IRF3_CHICK | Interferon regulatory factor 3; | KEGG:gga:396330 | KO:K09447 |
| DN5214_c0_g1_i6 | CF062_MOUSE | Uncharacterized protein C6orf62 homolog; | KEGG:mmu:79555 | NA |
| DN9772_c0_g1_i10 | UQCC2_DANRE | Ubiquinol-cytochrome-c reductase complex assembly factor 2; | KEGG:dre:393731 | KO:K17682 |
| DN2228_c2_g1_i8 | BMPR2_MOUSE | Bone morphogenetic protein receptor type-2; | KEGG:mmu:12168 | KO:K04671 |
| DN4998_c0_g1_i2 | CNPY3_BOVIN | Protein canopy homolog 3; | KEGG:bta:510220 | KO:K22816 |
| DN14729_c0_g1_i4 | FREM1_HUMAN | FRAS1-related extracellular matrix protein 1 {ECO:0000305}; | KEGG:hsa:158326 | KO:K23380 |
| DN4239_c0_g1_i17 | MYCB2_MOUSE | E3 ubiquitin-protein ligase MYCBP2 {ECO:0000305}; | KEGG:mmu:105689 | KO:K10693 |
| DN220085_c0_g1_i2 | LAG3_MOUSE | Lymphocyte activation gene 3 protein {ECO:0000303|PubMed:8921170}; | KEGG:hsa:3902 | KO:K06565 |
| DN12331_c1_g1_i3 | LRIG3_HUMAN | Leucine-rich repeats and immunoglobulin-like domains protein 3; | KEGG:hsa:121227 | NA |
| DN611_c1_g1_i6 | LRRK2_HUMAN | Leucine-rich repeat serine/threonine-protein kinase 2; | KEGG:hsa:120892 | KO:K08844 |
| DN2458_c0_g1_i1 | DDX17_MOUSE | Probable ATP-dependent RNA helicase DDX17; | KEGG:mmu:67040 | KO:K13178 |
| DN1712_c0_g2_i10 | DCAF4_HUMAN | DDB1- and CUL4-associated factor 4; | KEGG:bta:511629 | KO:K11799 |
topGO.mappings <- readMappings("G:/Shared drives/RNA Seq Supershedder Project/BWTE DE manuscript/extData/GOdbTrans.txt", sep = "\t", IDsep = ",")
goEnrich <- function(targetComp, ...) {
DE.results <- dt.tib %>% filter(!!sym(targetComp) != 0)
all.genes <- sort(unique(as.character(rownames(tfit$p.value))))
int.genes <- DE.results$transcript
int.genes <- factor(as.integer(all.genes %in% int.genes))
names(int.genes) = all.genes
go.obj.BP <- new("topGOdata", ontology='BP',
allGenes = int.genes,
annot = annFUN.gene2GO,
nodeSize = 5,
gene2GO = topGO.mappings)
go.obj.MF <- new("topGOdata", ontology='MF',
allGenes = int.genes,
annot = annFUN.gene2GO,
nodeSize = 5,
gene2GO = topGO.mappings)
go.obj.CC <- new("topGOdata", ontology='CC',
allGenes = int.genes,
annot = annFUN.gene2GO,
nodeSize = 5,
gene2GO = topGO.mappings)
results.BP <- runTest(go.obj.BP, algorithm = "elim", statistic = "fisher")
results.tab.BP <- GenTable(object = go.obj.BP,
elimFisher = results.BP,
topNodes = 50) %>%
as_tibble() %>%
mutate(pVal = as.numeric(elimFisher)) %>%
filter(pVal < 0.01) %>%
mutate(Domain = "BP") %>%
mutate(Comparison = targetComp)
results.MF <- runTest(go.obj.MF, algorithm = "elim", statistic = "fisher")
results.tab.MF <- GenTable(object = go.obj.MF,
elimFisher = results.MF,
topNodes = 50) %>%
as_tibble() %>%
mutate(pVal = as.numeric(elimFisher)) %>%
filter(pVal < 0.01) %>%
mutate(Domain = "MF") %>%
mutate(Comparison = targetComp)
results.CC <- runTest(go.obj.CC, algorithm = "elim", statistic = "fisher")
results.tab.CC <- GenTable(object = go.obj.CC,
elimFisher = results.CC,
topNodes = 50) %>%
as_tibble() %>%
mutate(pVal = as.numeric(elimFisher)) %>%
filter(pVal < 0.01) %>%
mutate(Domain = "CC") %>%
mutate(Comparison = targetComp)
rbind(results.tab.BP,
results.tab.MF,
results.tab.CC)
}
results <- list()
for(z in unique(names(dt.tib)[-1])) {
if (dt.tib %>%
filter(!!sym(z) != 0) %>%
nrow(.) > 0)
results[[length(results)+1]] <- goEnrich(z)
}
results.tib <- bind_rows(results, .id = "column_label") %>%
select(-column_label) %>%
arrange(GO.ID, Comparison)
kable(results.tib) %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
| GO.ID | Term | Annotated | Significant | Expected | elimFisher | pVal | Domain | Comparison |
|---|---|---|---|---|---|---|---|---|
| GO:0000381 | regulation of alternative mRNA splicing,… | 267 | 1 | 0.01 | 0.0062 | 6.20e-03 | BP | I1vI3 |
| GO:0001837 | epithelial to mesenchymal transition | 352 | 1 | 0.01 | 0.0082 | 8.20e-03 | BP | I1vI3 |
| GO:0002040 | sprouting angiogenesis | 319 | 3 | 0.34 | 0.00462 | 4.62e-03 | BP | CtlvI1 |
| GO:0003186 | tricuspid valve morphogenesis | 10 | 1 | 0.01 | 0.00536 | 5.36e-03 | BP | CtlvI3 |
| GO:0003252 | negative regulation of cell proliferatio… | 10 | 1 | 0.01 | 0.00536 | 5.36e-03 | BP | CtlvI3 |
| GO:0003724 | RNA helicase activity | 317 | 4 | 0.40 | 0.00069 | 6.90e-04 | MF | CtlvI1 |
| GO:0003724 | RNA helicase activity | 317 | 4 | 0.21 | 5.2e-05 | 5.20e-05 | MF | CtlvI3 |
| GO:0003724 | RNA helicase activity | 317 | 1 | 0.01 | 0.0077 | 7.70e-03 | MF | I1vI3 |
| GO:0003725 | double-stranded RNA binding | 250 | 5 | 0.32 | 1.6e-05 | 1.60e-05 | MF | CtlvI1 |
| GO:0003725 | double-stranded RNA binding | 250 | 3 | 0.16 | 0.00058 | 5.80e-04 | MF | CtlvI3 |
| GO:0003727 | single-stranded RNA binding | 335 | 4 | 0.42 | 0.00085 | 8.50e-04 | MF | CtlvI1 |
| GO:0003727 | single-stranded RNA binding | 335 | 3 | 0.22 | 0.00134 | 1.34e-03 | MF | CtlvI3 |
| GO:0003924 | GTPase activity | 866 | 10 | 1.09 | 1.1e-07 | 1.00e-07 | MF | CtlvI1 |
| GO:0003924 | GTPase activity | 866 | 7 | 0.57 | 1.1e-06 | 1.10e-06 | MF | CtlvI3 |
| GO:0003968 | RNA-directed 5’-3’ RNA polymerase activi… | 11 | 2 | 0.01 | 8.5e-05 | 8.50e-05 | MF | CtlvI1 |
| GO:0004127 | cytidylate kinase activity | 12 | 3 | 0.02 | 4.1e-07 | 4.00e-07 | MF | CtlvI1 |
| GO:0004127 | cytidylate kinase activity | 12 | 1 | 0.01 | 0.00783 | 7.83e-03 | MF | CtlvI3 |
| GO:0004550 | nucleoside diphosphate kinase activity | 41 | 3 | 0.05 | 1.9e-05 | 1.90e-05 | MF | CtlvI1 |
| GO:0004798 | thymidylate kinase activity | 9 | 3 | 0.01 | 1.6e-07 | 2.00e-07 | MF | CtlvI1 |
| GO:0004798 | thymidylate kinase activity | 9 | 1 | 0.01 | 0.00588 | 5.88e-03 | MF | CtlvI3 |
| GO:0005026 | transforming growth factor beta receptor… | 10 | 1 | 0.01 | 0.00653 | 6.53e-03 | MF | CtlvI3 |
| GO:0005525 | GTP binding | 1111 | 10 | 1.40 | 1.1e-06 | 1.10e-06 | MF | CtlvI1 |
| GO:0005525 | GTP binding | 1111 | 7 | 0.73 | 5.6e-06 | 5.60e-06 | MF | CtlvI3 |
| GO:0005811 | lipid droplet | 227 | 3 | 0.27 | 0.00251 | 2.51e-03 | CC | CtlvI1 |
| GO:0006165 | nucleoside diphosphate phosphorylation | 359 | 3 | 0.38 | 0.00640 | 6.40e-03 | BP | CtlvI1 |
| GO:0006227 | dUDP biosynthetic process | 9 | 3 | 0.01 | 9.1e-08 | 1.00e-07 | BP | CtlvI1 |
| GO:0006227 | dUDP biosynthetic process | 9 | 1 | 0.00 | 0.00483 | 4.83e-03 | BP | CtlvI3 |
| GO:0006233 | dTDP biosynthetic process | 9 | 3 | 0.01 | 9.1e-08 | 1.00e-07 | BP | CtlvI1 |
| GO:0006233 | dTDP biosynthetic process | 9 | 1 | 0.00 | 0.00483 | 4.83e-03 | BP | CtlvI3 |
| GO:0006235 | dTTP biosynthetic process | 11 | 3 | 0.01 | 1.8e-07 | 2.00e-07 | BP | CtlvI1 |
| GO:0006235 | dTTP biosynthetic process | 11 | 1 | 0.01 | 0.00590 | 5.90e-03 | BP | CtlvI3 |
| GO:0007026 | negative regulation of microtubule depol… | 114 | 2 | 0.12 | 0.00646 | 6.46e-03 | BP | CtlvI1 |
| GO:0009041 | uridylate kinase activity | 14 | 3 | 0.02 | 6.8e-07 | 7.00e-07 | MF | CtlvI1 |
| GO:0009041 | uridylate kinase activity | 14 | 1 | 0.01 | 0.00913 | 9.13e-03 | MF | CtlvI3 |
| GO:0010507 | negative regulation of autophagy | 214 | 2 | 0.11 | 0.00587 | 5.87e-03 | BP | CtlvI3 |
| GO:0010586 | miRNA metabolic process | 111 | 1 | 0.00 | 0.0026 | 2.60e-03 | BP | I1vI3 |
| GO:0014916 | regulation of lung blood pressure | 7 | 1 | 0.00 | 0.00376 | 3.76e-03 | BP | CtlvI3 |
| GO:0016540 | protein autoprocessing | 39 | 2 | 0.04 | 0.00078 | 7.80e-04 | BP | CtlvI1 |
| GO:0019012 | virion | 131 | 7 | 0.16 | 0.00466 | 4.66e-03 | CC | CtlvI1 |
| GO:0019031 | viral envelope | 33 | 2 | 0.04 | 0.00071 | 7.10e-04 | CC | CtlvI1 |
| GO:0019031 | viral envelope | 33 | 2 | 0.02 | 0.0002 | 2.00e-04 | CC | CtlvI3 |
| GO:0019056 | modulation by virus of host transcriptio… | 5 | 3 | 0.01 | 1.1e-08 | 0.00e+00 | BP | CtlvI1 |
| GO:0019062 | virion attachment to host cell | 43 | 2 | 0.05 | 0.00095 | 9.50e-04 | BP | CtlvI1 |
| GO:0019062 | virion attachment to host cell | 43 | 2 | 0.02 | 0.00025 | 2.50e-04 | BP | CtlvI3 |
| GO:0019064 | fusion of virus membrane with host plasm… | 33 | 2 | 0.03 | 0.00056 | 5.60e-04 | BP | CtlvI1 |
| GO:0019064 | fusion of virus membrane with host plasm… | 33 | 2 | 0.02 | 0.00014 | 1.40e-04 | BP | CtlvI3 |
| GO:0019065 | receptor-mediated endocytosis of virus b… | 10 | 2 | 0.01 | 4.8e-05 | 4.80e-05 | BP | CtlvI1 |
| GO:0019065 | receptor-mediated endocytosis of virus b… | 10 | 2 | 0.01 | 1.2e-05 | 1.20e-05 | BP | CtlvI3 |
| GO:0019076 | viral release from host cell | 98 | 4 | 0.10 | 3.6e-06 | 3.60e-06 | BP | CtlvI1 |
| GO:0019076 | viral release from host cell | 98 | 4 | 0.05 | 2.2e-07 | 2.00e-07 | BP | CtlvI3 |
| GO:0019083 | viral transcription | 296 | 3 | 0.31 | 0.00375 | 3.75e-03 | BP | CtlvI1 |
| GO:0020002 | host cell plasma membrane | 94 | 4 | 0.11 | 5.0e-06 | 5.00e-06 | CC | CtlvI1 |
| GO:0020002 | host cell plasma membrane | 94 | 4 | 0.06 | 3.9e-07 | 4.00e-07 | CC | CtlvI3 |
| GO:0021785 | branchiomotor neuron axon guidance | 15 | 1 | 0.01 | 0.00803 | 8.03e-03 | BP | CtlvI3 |
| GO:0022028 | tangential migration from the subventric… | 17 | 1 | 0.01 | 0.00910 | 9.10e-03 | BP | CtlvI3 |
| GO:0030430 | host cell cytoplasm | 102 | 3 | 0.12 | 0.00025 | 2.50e-04 | CC | CtlvI1 |
| GO:0030520 | intracellular estrogen receptor signalin… | 135 | 1 | 0.00 | 0.0032 | 3.20e-03 | BP | I1vI3 |
| GO:0030521 | androgen receptor signaling pathway | 169 | 1 | 0.00 | 0.0039 | 3.90e-03 | BP | I1vI3 |
| GO:0030683 | mitigation of host immune response by vi… | 6 | 1 | 0.01 | 0.00629 | 6.29e-03 | BP | CtlvI1 |
| GO:0030683 | mitigation of host immune response by vi… | 6 | 1 | 0.00 | 0.00322 | 3.22e-03 | BP | CtlvI3 |
| GO:0032473 | cytoplasmic side of mitochondrial outer … | 7 | 1 | 0.00 | 0.0044 | 4.40e-03 | CC | CtlvI3 |
| GO:0032474 | otolith morphogenesis | 18 | 1 | 0.01 | 0.00963 | 9.63e-03 | BP | CtlvI3 |
| GO:0034154 | toll-like receptor 7 signaling pathway | 19 | 3 | 0.02 | 1.0e-06 | 1.00e-06 | BP | CtlvI1 |
| GO:0034165 | positive regulation of toll-like recepto… | 11 | 3 | 0.01 | 1.8e-07 | 2.00e-07 | BP | CtlvI1 |
| GO:0034211 | GTP-dependent protein kinase activity | 8 | 1 | 0.01 | 0.00522 | 5.22e-03 | MF | CtlvI3 |
| GO:0035279 | mRNA cleavage involved in gene silencing… | 8 | 1 | 0.01 | 0.00838 | 8.38e-03 | BP | CtlvI1 |
| GO:0035564 | regulation of kidney size | 11 | 1 | 0.01 | 0.00590 | 5.90e-03 | BP | CtlvI3 |
| GO:0035666 | TRIF-dependent toll-like receptor signal… | 59 | 2 | 0.06 | 0.00178 | 1.78e-03 | BP | CtlvI1 |
| GO:0035712 | T-helper 2 cell activation | 7 | 1 | 0.01 | 0.00734 | 7.34e-03 | BP | CtlvI1 |
| GO:0035713 | response to nitrogen dioxide | 6 | 1 | 0.01 | 0.00629 | 6.29e-03 | BP | CtlvI1 |
| GO:0036122 | BMP binding | 13 | 1 | 0.01 | 0.00848 | 8.48e-03 | MF | CtlvI3 |
| GO:0036479 | peroxidase inhibitor activity | 5 | 1 | 0.00 | 0.00327 | 3.27e-03 | MF | CtlvI3 |
| GO:0039507 | suppression by virus of host molecular f… | 14 | 4 | 0.01 | 1.1e-09 | 0.00e+00 | BP | CtlvI1 |
| GO:0039513 | suppression by virus of host catalytic a… | 10 | 1 | 0.01 | 0.00536 | 5.36e-03 | BP | CtlvI3 |
| GO:0039519 | modulation by virus of host autophagy | 9 | 1 | 0.01 | 0.00942 | 9.42e-03 | BP | CtlvI1 |
| GO:0039519 | modulation by virus of host autophagy | 9 | 1 | 0.00 | 0.00483 | 4.83e-03 | BP | CtlvI3 |
| GO:0039657 | suppression by virus of host gene expres… | 25 | 4 | 0.03 | 1.3e-08 | 0.00e+00 | BP | CtlvI1 |
| GO:0039694 | viral RNA genome replication | 103 | 3 | 0.11 | 0.00018 | 1.80e-04 | BP | CtlvI1 |
| GO:0039706 | co-receptor binding | 9 | 1 | 0.01 | 0.00588 | 5.88e-03 | MF | CtlvI3 |
| GO:0042025 | host cell nucleus | 34 | 6 | 0.04 | 2.7e-12 | 0.00e+00 | CC | CtlvI1 |
| GO:0042025 | host cell nucleus | 34 | 3 | 0.02 | 1.4e-06 | 1.40e-06 | CC | CtlvI3 |
| GO:0042289 | MHC class II protein binding | 11 | 1 | 0.01 | 0.00718 | 7.18e-03 | MF | CtlvI3 |
| GO:0043367 | CD4-positive, alpha-beta T cell differen… | 239 | 4 | 0.25 | 0.00012 | 1.20e-04 | BP | CtlvI1 |
| GO:0043382 | positive regulation of memory T cell dif… | 5 | 1 | 0.01 | 0.00525 | 5.25e-03 | BP | CtlvI1 |
| GO:0043621 | protein self-association | 175 | 3 | 0.22 | 0.00142 | 1.42e-03 | MF | CtlvI1 |
| GO:0044753 | amphisome | 9 | 1 | 0.01 | 0.0057 | 5.70e-03 | CC | CtlvI3 |
| GO:0045071 | negative regulation of viral genome repl… | 136 | 5 | 0.14 | 3.3e-07 | 3.00e-07 | BP | CtlvI1 |
| GO:0045085 | negative regulation of interleukin-2 bio… | 13 | 1 | 0.01 | 0.00696 | 6.96e-03 | BP | CtlvI3 |
| GO:0045087 | innate immune response | 1505 | 13 | 1.58 | 8.1e-07 | 8.00e-07 | BP | CtlvI1 |
| GO:0045087 | innate immune response | 1505 | 8 | 0.81 | 4.5e-05 | 4.50e-05 | BP | CtlvI3 |
| GO:0045111 | intermediate filament cytoskeleton | 311 | 4 | 0.37 | 0.00052 | 5.20e-04 | CC | CtlvI1 |
| GO:0045111 | intermediate filament cytoskeleton | 311 | 3 | 0.20 | 0.0010 | 1.00e-03 | CC | CtlvI3 |
| GO:0045445 | myoblast differentiation | 227 | 1 | 0.01 | 0.0053 | 5.30e-03 | BP | I1vI3 |
| GO:0045590 | negative regulation of regulatory T cell… | 8 | 1 | 0.01 | 0.00838 | 8.38e-03 | BP | CtlvI1 |
| GO:0045590 | negative regulation of regulatory T cell… | 8 | 1 | 0.00 | 0.00429 | 4.29e-03 | BP | CtlvI3 |
| GO:0045906 | negative regulation of vasoconstriction | 12 | 1 | 0.01 | 0.00643 | 6.43e-03 | BP | CtlvI3 |
| GO:0046598 | positive regulation of viral entry into … | 28 | 2 | 0.03 | 0.00040 | 4.00e-04 | BP | CtlvI1 |
| GO:0046718 | viral entry into host cell | 262 | 4 | 0.14 | 0.00523 | 5.23e-03 | BP | CtlvI3 |
| GO:0046755 | viral budding | 74 | 4 | 0.08 | 1.2e-06 | 1.20e-06 | BP | CtlvI1 |
| GO:0046755 | viral budding | 74 | 4 | 0.04 | 7.1e-08 | 1.00e-07 | BP | CtlvI3 |
| GO:0048295 | positive regulation of isotype switching… | 8 | 1 | 0.01 | 0.00838 | 8.38e-03 | BP | CtlvI1 |
| GO:0048842 | positive regulation of axon extension in… | 15 | 1 | 0.01 | 0.00803 | 8.03e-03 | BP | CtlvI3 |
| GO:0050709 | negative regulation of protein secretion | 312 | 3 | 0.33 | 0.00434 | 4.34e-03 | BP | CtlvI1 |
| GO:0051024 | positive regulation of immunoglobulin se… | 7 | 1 | 0.01 | 0.00734 | 7.34e-03 | BP | CtlvI1 |
| GO:0051539 | 4 iron, 4 sulfur cluster binding | 170 | 3 | 0.21 | 0.00131 | 1.31e-03 | MF | CtlvI1 |
| GO:0051607 | defense response to virus | 526 | 12 | 0.55 | 1.1e-09 | 0.00e+00 | BP | CtlvI1 |
| GO:0051865 | protein autoubiquitination | 241 | 4 | 0.25 | 0.00012 | 1.20e-04 | BP | CtlvI1 |
| GO:0051900 | regulation of mitochondrial depolarizati… | 42 | 2 | 0.02 | 0.00023 | 2.30e-04 | BP | CtlvI3 |
| GO:0052027 | modulation by symbiont of host signal tr… | 6 | 1 | 0.01 | 0.00629 | 6.29e-03 | BP | CtlvI1 |
| GO:0052027 | modulation by symbiont of host signal tr… | 6 | 1 | 0.00 | 0.00322 | 3.22e-03 | BP | CtlvI3 |
| GO:0055036 | virion membrane | 32 | 5 | 0.04 | 3.8e-10 | 0.00e+00 | CC | CtlvI1 |
| GO:0055036 | virion membrane | 32 | 5 | 0.02 | 1.4e-11 | 0.00e+00 | CC | CtlvI3 |
| GO:0060161 | positive regulation of dopamine receptor… | 13 | 1 | 0.01 | 0.00696 | 6.96e-03 | BP | CtlvI3 |
| GO:0060338 | regulation of type I interferon-mediated… | 100 | 3 | 0.11 | 0.00016 | 1.60e-04 | BP | CtlvI1 |
| GO:0060338 | regulation of type I interferon-mediated… | 100 | 2 | 0.05 | 0.00132 | 1.32e-03 | BP | CtlvI3 |
| GO:0060349 | bone morphogenesis | 227 | 2 | 0.12 | 0.00658 | 6.58e-03 | BP | CtlvI3 |
| GO:0060700 | regulation of ribonuclease activity | 13 | 2 | 0.01 | 8.4e-05 | 8.40e-05 | BP | CtlvI1 |
| GO:0060836 | lymphatic endothelial cell differentiati… | 12 | 1 | 0.01 | 0.00643 | 6.43e-03 | BP | CtlvI3 |
| GO:0061614 | pri-miRNA transcription by RNA polymeras… | 116 | 1 | 0.00 | 0.0027 | 2.70e-03 | BP | I1vI3 |
| GO:0061626 | pharyngeal arch artery morphogenesis | 18 | 1 | 0.01 | 0.00963 | 9.63e-03 | BP | CtlvI3 |
| GO:0071222 | cellular response to lipopolysaccharide | 438 | 4 | 0.46 | 0.00116 | 1.16e-03 | BP | CtlvI1 |
| GO:0072583 | clathrin-dependent endocytosis | 166 | 2 | 0.09 | 0.00359 | 3.59e-03 | BP | CtlvI3 |
| GO:0080008 | Cul4-RING E3 ubiquitin ligase complex | 128 | 1 | 0.00 | 0.0028 | 2.80e-03 | CC | CtlvI14 |
| GO:0080008 | Cul4-RING E3 ubiquitin ligase complex | 128 | 1 | 0.00 | 0.0028 | 2.80e-03 | CC | I5vI14 |
| GO:0097487 | multivesicular body, internal vesicle | 11 | 1 | 0.01 | 0.0070 | 7.00e-03 | CC | CtlvI3 |
| GO:0099400 | caveola neck | 5 | 1 | 0.00 | 0.0032 | 3.20e-03 | CC | CtlvI3 |
| GO:1900245 | positive regulation of MDA-5 signaling p… | 20 | 3 | 0.02 | 1.2e-06 | 1.20e-06 | BP | CtlvI1 |
| GO:1900245 | positive regulation of MDA-5 signaling p… | 20 | 3 | 0.01 | 1.5e-07 | 2.00e-07 | BP | CtlvI3 |
| GO:1900246 | positive regulation of RIG-I signaling p… | 31 | 3 | 0.03 | 4.8e-06 | 4.80e-06 | BP | CtlvI1 |
| GO:1900246 | positive regulation of RIG-I signaling p… | 31 | 3 | 0.02 | 6.0e-07 | 6.00e-07 | BP | CtlvI3 |
| GO:1901727 | positive regulation of histone deacetyla… | 17 | 1 | 0.01 | 0.00910 | 9.10e-03 | BP | CtlvI3 |
| GO:1901953 | positive regulation of anterograde dense… | 9 | 1 | 0.01 | 0.00942 | 9.42e-03 | BP | CtlvI1 |
| GO:1902499 | positive regulation of protein autoubiqu… | 9 | 1 | 0.00 | 0.00483 | 4.83e-03 | BP | CtlvI3 |
| GO:1902731 | negative regulation of chondrocyte proli… | 5 | 1 | 0.00 | 0.00268 | 2.68e-03 | BP | CtlvI3 |
| GO:1902823 | negative regulation of late endosome to … | 7 | 1 | 0.00 | 0.00376 | 3.76e-03 | BP | CtlvI3 |
| GO:1903125 | negative regulation of thioredoxin perox… | 5 | 1 | 0.00 | 0.00268 | 2.68e-03 | BP | CtlvI3 |
| GO:1903217 | negative regulation of protein processin… | 8 | 1 | 0.00 | 0.00429 | 4.29e-03 | BP | CtlvI3 |
| GO:1903744 | positive regulation of anterograde synap… | 9 | 1 | 0.01 | 0.00942 | 9.42e-03 | BP | CtlvI1 |
| GO:1903980 | positive regulation of microglial cell a… | 12 | 1 | 0.01 | 0.00643 | 6.43e-03 | BP | CtlvI3 |
| GO:1904713 | beta-catenin destruction complex binding | 7 | 1 | 0.00 | 0.00457 | 4.57e-03 | MF | CtlvI3 |
| GO:1904887 | Wnt signalosome assembly | 5 | 1 | 0.00 | 0.00268 | 2.68e-03 | BP | CtlvI3 |
| GO:1905279 | regulation of retrograde transport, endo… | 8 | 1 | 0.00 | 0.00429 | 4.29e-03 | BP | CtlvI3 |
| GO:1905289 | regulation of CAMKK-AMPK signaling casca… | 10 | 1 | 0.01 | 0.00536 | 5.36e-03 | BP | CtlvI3 |
| GO:2000051 | negative regulation of non-canonical Wnt… | 17 | 3 | 0.02 | 7.3e-07 | 7.00e-07 | BP | CtlvI1 |
| GO:2000172 | regulation of branching morphogenesis of… | 18 | 1 | 0.01 | 0.00963 | 9.63e-03 | BP | CtlvI3 |
| GO:2000553 | positive regulation of T-helper 2 cell c… | 18 | 3 | 0.02 | 8.8e-07 | 9.00e-07 | BP | CtlvI1 |
| GO:2001014 | regulation of skeletal muscle cell diffe… | 62 | 2 | 0.03 | 0.00051 | 5.10e-04 | BP | CtlvI3 |
| GO:2001014 | regulation of skeletal muscle cell diffe… | 62 | 1 | 0.00 | 0.0014 | 1.40e-03 | BP | I1vI3 |